Min Python version >= 3.9 for users & >= 3.10 for developers

.github/workflows/alltests.yml

@@ -8,6 +8,13 @@ on:
       - master
   workflow_dispatch:
 
+# CodeQL "Workflow does not contain permissions": restrict the GITHUB_TOKEN to
+# the minimum. These jobs only read the repo -- checkout, conda/python setup,
+# caching, and tests. Codecov uploads authenticate with CODECOV_TOKEN, not the
+# GITHUB_TOKEN, so no write scope is needed.
+permissions:
+  contents: read
+
 concurrency:
   # Keep push and pull_request runs separate so same-SHA PR updates do not inherit cancelled push checks.
   group: alltests-${{ github.event_name }}-${{ github.event.pull_request.head.repo.full_name || github.repository }}-${{ github.head_ref || github.ref_name }}
@@ -68,9 +75,36 @@ jobs:
       - uses: conda-incubator/setup-miniconda@v3
         with:
           miniconda-version: "latest"
-          auto-activate-base: true
+          python-version: ${{ matrix.python-version }}
+          channels: conda-forge
+          auto-activate-base: false
+          # Name the env explicitly: without this the active environment is
+          # ambiguous (base vs the auto-created `test`), which can leave pip
+          # and python pointing at different prefixes.
+          activate-environment: qmcpy-ci
           conda-remove-defaults: true
-          use-only-tar-bz2: true
+
+      # Without python-version above, matrix.python-version reached only the job
+      # name and every job ran the conda base interpreter. Steps touching Python
+      # must use a profile-loading shell (bash -el / pwsh) to see the env.
+      - name: Verify interpreter matches the matrix (Unix)
+        if: runner.os != 'Windows'
+        shell: bash -el {0}
+        run: |
+          echo "which python : $(which python)"
+          echo "which pip    : $(which pip)"
+          conda info --envs || true
+          python -c "import sys; print('prefix:',sys.prefix); print(sys.version)"
+          python -c "import sys; got='.'.join(map(str,sys.version_info[:2])); want='${{ matrix.python-version }}'; assert got==want, 'matrix says %s but interpreter is %s'%(want,got)"
+
+      - name: Verify interpreter matches the matrix (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          Get-Command python | Format-List
+          conda info --envs
+          python -c "import sys; print('prefix:',sys.prefix); print(sys.version)"
+          python -c "import sys; got='.'.join(map(str,sys.version_info[:2])); want='${{ matrix.python-version }}'; assert got==want, 'matrix says %s but interpreter is %s'%(want,got)"
 
       # -----------------------------------------------------------
       # Clean old coverage files
@@ -222,18 +256,22 @@ jobs:
 
       - name: Build and cache wheels (Linux)
         if: runner.os == 'Linux'
+        shell: bash -el {0}
         run: |
-          python -m pip wheel -w ./.wheels .[test,test_torch,test_gpytorch,test_botorch,test_umbridge] || true
+          python -m pip wheel -w ./.wheels ".[test,test_torch,test_gpytorch,test_botorch,test_umbridge]" || true
       - name: Install Python dependencies (Linux)
         if: runner.os == 'Linux'
+        shell: bash -el {0}
         run: |
           pip install --find-links ./.wheels -e ".[test,test_torch,test_gpytorch,test_botorch,test_umbridge]"
       - name: Build and cache wheels (macOS)
         if: runner.os == 'macOS'
+        shell: bash -el {0}
         run: |
-          python -m pip wheel -w ./.wheels .[test,test_torch,test_gpytorch,test_botorch] || true
+          python -m pip wheel -w ./.wheels ".[test,test_torch,test_gpytorch,test_botorch]" || true
       - name: Install Python dependencies (macOS)
         if: runner.os == 'macOS'
+        shell: bash -el {0}
         run: |
           pip install --find-links ./.wheels -e ".[test,test_torch,test_gpytorch,test_botorch]"
       - name: Build and cache wheels (Windows)
@@ -246,12 +284,25 @@ jobs:
         shell: pwsh
         run: |
           pip install --find-links ./.wheels -e '.[test,test_torch,test_gpytorch,test_botorch]'
-      - name: Install MPMC dependencies
-        run: |
-          qmcpy-install-mpmc
-      - name: Validate MPMC dependencies
-        run: |
-          python -c "import torch, pyg_lib, torch_geometric; print(f'torch={torch.__version__}'); print('MPMC dependencies ready')"
+      - name: Install MPMC dependencies (Unix)
+        if: runner.os != 'Windows'
+        shell: bash -el {0}
+        run: qmcpy-install-mpmc
+
+      - name: Install MPMC dependencies (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: qmcpy-install-mpmc
+
+      - name: Validate MPMC dependencies (Unix)
+        if: runner.os != 'Windows'
+        shell: bash -el {0}
+        run: python -c "import torch, pyg_lib, torch_geometric; print(f'torch={torch.__version__}'); print('MPMC dependencies ready')"
+
+      - name: Validate MPMC dependencies (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: python -c "import torch, pyg_lib, torch_geometric; print(f'torch={torch.__version__}'); print('MPMC dependencies ready')"
       # -----------------------------------------------------------
       # Install minimal LaTeX required by Jupyter notebooks (OS-specific)
       # -----------------------------------------------------------
@@ -375,7 +426,7 @@ jobs:
             Invoke-WithRetry -Description "Refresh MiKTeX package database" -Script {
               mpm --admin --update-db
             }
-            $packages = @('latexmk','dvipng','cm-super','lmodern','type1cm','tex-gyre')
+            $packages = @('latexmk','dvipng','cm-super','lmodern','type1cm','tex-gyre','l3backend')
             foreach ($pkg in $packages) {
               Invoke-WithRetry -Description "Install MiKTeX package $pkg" -Script {
                 mpm --admin --install=$pkg
@@ -386,19 +437,71 @@ jobs:
           Invoke-WithRetry -Description "Refresh MiKTeX filename database" -Script {
             initexmf --admin --update-fndb
           }
+          $L3BackendPath = kpsewhich l3backend-dvips.def
+          if ([string]::IsNullOrWhiteSpace($L3BackendPath)) {
+            throw "MiKTeX install did not provide l3backend-dvips.def"
+          }
           latex --version
           latexmk -v
           dvipng --version
 
       # -----------------------------------------------------------
       # Run doctests (OS-specific)
       # -----------------------------------------------------------
-      - run: pip freeze
-      - run: make doctests_minimal
-      - run: make doctests_torch
-      - run: make doctests_gpytorch
-      - run: make doctests_botorch
-      - run: make doctests_markdown
+      - name: pip freeze (Unix)
+        if: runner.os != 'Windows'
+        shell: bash -el {0}
+        run: pip freeze
+
+      - name: pip freeze (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: pip freeze
+      - name: doctests_minimal (Unix)
+        if: runner.os != 'Windows'
+        shell: bash -el {0}
+        run: make doctests_minimal
+
+      - name: doctests_minimal (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: make doctests_minimal
+      - name: doctests_torch (Unix)
+        if: runner.os != 'Windows'
+        shell: bash -el {0}
+        run: make doctests_torch
+
+      - name: doctests_torch (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: make doctests_torch
+      - name: doctests_gpytorch (Unix)
+        if: runner.os != 'Windows'
+        shell: bash -el {0}
+        run: make doctests_gpytorch
+
+      - name: doctests_gpytorch (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: make doctests_gpytorch
+      - name: doctests_botorch (Unix)
+        if: runner.os != 'Windows'
+        shell: bash -el {0}
+        run: make doctests_botorch
+
+      - name: doctests_botorch (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: make doctests_botorch
+      - name: doctests_markdown (Unix)
+        if: runner.os != 'Windows'
+        shell: bash -el {0}
+        run: make doctests_markdown
+
+      - name: doctests_markdown (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: make doctests_markdown
       - name: Run umbridge doctests on Linux full sweeps when Docker is available
         shell: bash -l {0}
         run: |
@@ -411,12 +514,26 @@ jobs:
           else
             echo "Skipping umbridge doctests because Docker is not available on this runner"
           fi
-      - name: Run MPMC doctests
+      - name: Run MPMC doctests (Unix)
+        if: runner.os != 'Windows'
+        shell: bash -el {0}
+        run: make doctests_mpmc
+
+      - name: Run MPMC doctests (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
         run: make doctests_mpmc
       # -----------------------------------------------------------
       # Run unittests for Python source files
       # -----------------------------------------------------------
-      - name: Run unittests (parallel)
+      - name: Run unittests (parallel, Unix)
+        if: runner.os != 'Windows'
+        shell: bash -el {0}
+        run: make unittests
+
+      - name: Run unittests (parallel, Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
         run: make unittests
 
       # -----------------------------------------------------------